If we have a module using the ‘groovy’ plugin and we have both java and groovy under the same source-set, the plugin first compiles the Java classes, then deletes the output and compiles the Groovy classes.
In our case, we tried to separate the code, as we wanted to make sure that the Java classes do not depend on Groovy. As a minimum, Gradle should have warned us. Ideally it should have preserved the Java classes and added the Groovy classes.
Using Gradle Wrapper, Gradle 1.6, JDK 1.6_u33, RHEL 5